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At least 343 records · Page 19Linked to original sources
arXiv2016

Interspecific allometric scaling of unicellular organisms as an evolutionary process of food chain creation

Metabolism of living organisms is a foundation of life. The metabolic rate (energy production per unit time) increases slower than organisms' mass. When this phenomenon is considered across different species, it is called interspecific allometric scaling, whose causes are unknown. We argue that the cause of interspecific allometric scaling is the total effect of physiological and adaptation mechanisms inherent to organisms composing a food chain. Together, the workings of these mechanisms are united by a primary goal of any living creature - its successful reproduction. This primary necessity of each organism and of the entire food chain is that common denominator, to which all organisms adjust their metabolic rates. In this article, we consider unicellular organisms, while the second paper studies multicellular organisms and the entire concept in more detail. Here, using the proposed concepts and experimentally verified growth models of five different unicellular organisms, we obtain close to experimental findings values of allometric exponents of 0.757 for the end of growth and 0.853 for the beginning of growth. These results comply with experimental observations and prove our theory that the requirement of successful reproduction within the food chain is an important factor shaping interspecific allometric scaling.

q-bio.OT↗
arXiv2016

A quantitative definition of organismality and its application to lichen

The organism is a fundamental concept in biology. However there is no universally accepted, formal, and yet broadly applicable definition of what an organism is. Here we introduce a candidate definition. We adopt the view that the "organism" is a functional concept, used by scientists to address particular questions concerning the future state of a biological system, rather than something wholly defined by that system. In this approach organisms are a coarse-graining of a fine-grained dynamical model of a biological system. Crucially, the coarse-graining of the system into organisms is chosen so that their dynamics can be used by scientists to make accurate predictions of those features of the biological system that interests them, and do so with minimal computational burden. To illustrate our framework we apply it to a dynamic model of lichen symbiosis---a system where either the lichen or its constituent fungi and algae could reasonably be considered "organisms." We find that the best choice for what organisms are in this scenario are complex mixtures of many entities that do not resemble standard notions of organisms. When we restrict our allowed coarse-grainings to more traditional types of organisms, we find that ecological conditions, such as niche competition and predation pressure, play a significant role in determining the best choice for organisms.

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arXiv2016

Rethinking the Experiment

The crisis in the reproducibility of experiments invites a re-evaluation of methods of inquiry and validation procedures. The text challenges current assumptions of knowledge acquisition and introduces G-complexity for defining decidable vs. non-decidable knowledge domains. A "second Cartesian revolution," informed by and in awareness of anticipatory processes, should result in scientific methods that transcend determinism and reductionism. Physics and physics-based disciplines convincingly ascertained themselves by adequately describing the non-living. A complementary perspective should account for the specific causality characteristic of life by integrating past, present, and future. Knowledge about anticipatory processes facilitates attainment of this goal. Society cannot afford the dead-end street of reductionism. Science, itself an expression of anticipatory activity, makes possible in our days alternative understandings of reality and its dynamics.

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arXiv2016

The design of a proto-animal brain based upon spike timing

A basal animal model is described as an organism similar to a Limpet that is attached to the sea floor living in a reproductive community. Its brain model uses logic cells (gates) to create a high frequency spike generator. Addition logic cells create a timing framework based upon Pulse Width Modulation (PWM), and create multi-cell, spike driven muscle actuators and bi-directional shift registers that serve as memories. Together, these logic cells generate a pulse train that forms a recurrent fractal in the form of coherent square waves that consist of an equal number of set pulses and reset pulses. These pulses drive the actuators that pump water and food through its shell. Some of these individuals lose their permanent attachment to the sea floor, and evolve the ability to move around using the feeding motions. This creates the hazard of getting stuck against an object or moving away from its breeding community. They evolve a sensor system and logic cells that produce a restoring motion for each avoidance motion. This keeps the animal in the specific region of an object that it encounters (hefting), and maintains the zero sum (coherence) of the fractal, and connects the organism cyberneticly to objects that are sensed in its environment. The logic units evolve to store permanent memories, and add plus and minus pulse trains together into a single pulse train that allow the animal to follow a moving object (imprinting). Additional logic units evolve that allow the animal to heft using contacts with multiple objects that allow the animal to return to its point of origin (reproductive migration) using permanent memories that are created when a pulse is not reset to zero.So, information is stored in multiple logic cells instead of a connection to one logic cell, and is based upon spike timing rather than static (synaptic) connections between cells.

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arXiv2016

Flux ratios and channel structures

We investigate Ussing's unidirectional fluxes and flux ratios of charged tracers motivated particularly by the insightful proposal of Hodgkin and Keynes on a relation between flux ratios and channel structure. Our study is based on analysis of quasi-one-dimensional Poisson-Nernst-Planck type models for ionic flows through membrane channels. This class of models includes the Poisson equation that determines the electrical potential from the charges present and is in that sense consistent. Ussing's flux ratios generally depend on all physical parameters involved in ionic flows, particularly, on bulk conditions and channel structures. Certain setups of ion channel experiments result in flux ratios that are universal in the sense that their values depend on bulk conditions but not on channel structures; other setups lead to flux ratios that are specific in the sense that their values depend on channel structures too. Universal flux ratios could serve some purposes better than specific flux ratios in some circumstances and worse in other circumstances. We focus on two treatments of tracer flux measurements that serve as estimators of important properties of ion channels. The first estimator determines the flux of the main ion species from measurements of the flux of its tracer. Our analysis suggests a better experimental design so that the flux ratio of the tracer flux and the main ion flux is universal. The second treatment of tracer fluxes concerns ratios of fluxes and experimental setups that try to determine some properties of channel structure. We analyze the two widely used experimental designs of estimating flux ratios and show that the most widely used method depends on the spatial distribution of permanent charge so this flux ratio is specific and thus allows estimation of (some of) the properties of that permanent charge, even with ideal ionic solutions. ...

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arXiv2017

What Are People Tweeting about Zika? An Exploratory Study Concerning Symptoms, Treatment, Transmission, and Prevention

The purpose of this study was to do a dataset distribution analysis, a classification performance analysis, and a topical analysis concerning what people are tweeting about four disease characteristics: symptoms, transmission, prevention, and treatment. A combination of natural language processing and machine learning techniques were used to determine what people are tweeting about Zika. Specifically, a two-stage classifier system was built to find relevant tweets on Zika, and then categorize these into the four disease categories. Tweets in each disease category were then examined using latent dirichlet allocation (LDA) to determine the five main tweet topics for each disease characteristic. Results 1,234,605 tweets were collected. Tweets by males and females were similar (28% and 23% respectively). The classifier performed well on the training and test data for relevancy (F=0.87 and 0.99 respectively) and disease characteristics (F=0.79 and 0.90 respectively). Five topics for each category were found and discussed with a focus on the symptoms category. Through this process, we demonstrate how misinformation can be discovered so that public health officials can respond to the tweets with misinformation.

cs.SI↗
arXiv2017

Metrics and Harmonic Analysis on DNA

A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not trivial distance between two sequences and to perform the Discrete Fourier Transform on a sequence. Using the definition of distance the sequence of $β$-globin for Homo, Gallus and Opossum are compared. The Discrete Fourier Transform for some simple examples is computed.

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arXiv2017

CHROTRAN: A mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death. Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.

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arXiv2018

Doing Things Twice (Or Differently): Strategies to Identify Studies for Targeted Validation

The "reproducibility crisis" has been a highly visible source of scientific controversy and dispute. Here, I propose and review several avenues for identifying and prioritizing research studies for the purpose of targeted validation. Of the various proposals discussed, I identify scientific data science as being a strategy that merits greater attention among those interested in reproducibility. I argue that the tremendous potential of scientific data science for uncovering high-value research studies is a significant and rarely discussed benefit of the transition to a fully open-access publishing model.

cs.CY↗
arXiv2017

Biochemical mechanism of resistance in some Brassica genotypes against Lipaphis erysimi (Kaltenbach) (Homoptera: Aphididae)

Two years study was carried out during 2006-07 and 2007-08 crop seasons to study the response of different genotypes of oilseeds Brassica to Lipaphis erysimi (Kaltenbach) infestation both under field and screen house conditions and to find out the relationship of various biochemical constituents to aphid infestation. Among the various genotypes, the population of L. erysimi was significantly high on Brassica rapa variety brown sarson cv. BSH 1 and B. rapa var. yellow sarson cv. YST 151 in unprotected set i.e. 53.7 and 52.3 aphids/ plant, respectively. However, it was the lowest on Eruca sativa cv. T 27 (4.7 aphids/plant) followed by B. carinata cv. DLSC 2 (20.9 aphids/ plant) which suffered the least yield loss i.e. 5.79 and 10.59 per cent, respectively. Almost similar trend was observed in seedling mortality, which was the maximum in BSH 1 and YST 151, while no seedling mortality was observed in the case of T 27 during both the years of study. Analysis of various biochemical constituents revealed that glucosinolates, total phenols and ortho-dihydroxy phenols had inverse relationship with the aphid infestation. Higher amount of these biochemical constituents in T 27 and DLSC 2 was responsible for lower aphid infestation on these genotypes.

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arXiv2017

Measuring Light Pollution with Fisheye Lens Imagery from A Moving Boat, A Proof of Concept

Near all-sky imaging photometry was performed from a boat on the Gulf of Aqaba to measure the night sky brightness in a coastal environment. The boat was not anchored, and therefore drifted and rocked. The camera was mounted on a tripod without any inertia/motion stabilization. A commercial digital single lens reflex (DSLR) camera and fisheye lens were used with ISO setting of 6400, with the exposure time varied between 0.5 s and 5 s. We find that despite movement of the vessel the measurements produce quantitatively comparable results apart from saturation effects. We discuss the potential and limitations of this method for mapping light pollution in marine and freshwater systems. This work represents the proof of concept that all-sky photometry with a commercial DSLR camera is a viable tool to determine light pollution in an ecological context from a moving boat.

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arXiv2017

Symmetry and Minimum Principle at the Basis of the Genetic Code

The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has been proposed a few years ago. The present paper is a review of the model, of some of its first applications as well as of its recent developments. Indeed, after a motivated presentation of our mathematical model, we illustrate its pertinence by applying it for the elaboration and verification of sum rules for codon usage probabilities, as well as for establishing relations and some predictions between physical-chemical properties of amino-acids. Then, defining in this context a "bio-spin" structure for the nucleotides and codons, the interaction between a couple of codon-anticodon can simply be represented by a (bio) spin-spin potential. This approach will constitute the second part of the paper where, imposing the minimum energy principle, an analysis of the evolution of the genetic code can be performed with good agreement with the generally accepted scheme. A more precise study of this interaction model provides informations on codon bias, consistent with data.

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arXiv2017

About new hybrid approach in cancer modeling

In the present article we demonstrate a new hybrid model of tumor growth. Our model is stochastic by tumor population development and strongly deterministic in cell motility dynamics and spatial propagation. In addition, it has excellent extendibility property. Described model is tested on general behavior and on avascular tumor growth case qualitatively.

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arXiv2017

An applied mathematician's perspective on Rosennean Complexity

The theoretical biologist Robert Rosen developed a highly original approach for investigating the question "What is life?", the most fundamental problem of biology. Considering that Rosen made extensive use of mathematics it might seem surprising that his ideas have only rarely been implemented in mathematical models. On the one hand, Rosen propagates relational models that neglect underlying structural details of the components and focus on relationships between the elements of a biological system, according to the motto "throw away the physics, keep the organisation". Rosen's strong rejection of mechanistic models that he implicitly associates with a strong form of reductionism might have deterred mathematical modellers from adopting his ideas for their own work. On the other hand Rosen's presentation of his modelling framework, (M,R) systems, is highly abstract which makes it hard to appreciate how this approach could be applied to concrete biological problems. In this article, both the mathematics as well as those aspects of Rosen's work are analysed that relate to his philosophical ideas. It is shown that Rosen's relational models are a particular type of mechanistic model with specific underlying assumptions rather than a different kind of model that excludes mechanistic models. The strengths and weaknesses of relational models are investigated by comparison with current network biology literature. Finally, it is argued that Rosen's definition of life, "organisms are closed to efficient causation", should be considered as a hypothesis to be tested and ideas how this postulate could be implemented in mathematical models are presented.

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arXiv2017

Assembling sequences of DNA using an on-line algorithm based on DeBruijn graphs

The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of detecting similarities between animals, dangerous pests in crops, and so on. Some of the algorithms and data structures that have been created to solve this problem are Needleman Wunsch algorithm, DeBruijn graphs and greedy algorithms working on overlaps graphs; these try to work out the problem from different approaches that give place to certain advantages and disadvantages to be discussed. In this article we first expose a summary of the research done on already created solutions for the DNA assembly problem, to present later an on-line solution to the same matter, which, despite not considering mutations, would have the capacity of using only the necessary amount of readings to assemble an user specified amount of genes.

cs.DS↗